cNMA: a framework of encounter complex-based normal mode analysis to model conformational changes in protein interactions

Activities of many biological macromolecules involve large conformational transitions for which crystallography can specify atomic details of alternative end states, but the course of transitions is often beyond the reach of computations based on full-atomic potential functions. We have developed a coarse-grained force field for molecular mechanics calculations based on the virtual interactions of Cα atoms in protein molecules. This force field is parameterized based on the statistical distribution of the energy terms extracted from crystallographic data, and it is formulated to capture features dependent on secondary structure and on residue-specific contact information. The resulting force field is applied to energy minimization and normal mode analysis of several proteins. We find robust convergence in minimizations to low energies and energy gradients with low degrees of structural distortion, and atomic fluctuations calculated from the normal mode analyses correlate well with the experimental B-factors obtained from high-resolution crystal structures. These findings suggest that the virtual atom force field is a suitable tool for various molecular mechanics applications on large macromolecular systems undergoing large conformational changes.

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Protein conformational transitions explored by a morphing approach based on normal mode analysis in internal coordinates

PLoS ONE ◽

10.1371/journal.pone.0258818 ◽

2021 ◽

Vol 16 (11) ◽

pp. e0258818

Author(s):

Byung Ho Lee ◽

Soon Woo Park ◽

Soojin Jo ◽

Moon Ki Kim

Keyword(s):

Normal Mode ◽

Conformational Changes ◽

Degrees Of Freedom ◽

Large Scale ◽

Conformational Transition ◽

Normal Mode Analysis ◽

Mode Analysis ◽

Theoretical Approaches ◽

Internal Coordinates ◽

Transition Pathways

Large-scale conformational changes are essential for proteins to function properly. Given that these transition events rarely occur, however, it is challenging to comprehend their underlying mechanisms through experimental and theoretical approaches. In this study, we propose a new computational methodology called internal coordinate normal mode-guided elastic network interpolation (ICONGENI) to predict conformational transition pathways in proteins. Its basic approach is to sample intermediate conformations by interpolating the interatomic distance between two end-point conformations with the degrees of freedom constrained by the low-frequency dynamics afforded by normal mode analysis in internal coordinates. For validation of ICONGENI, it is applied to proteins that undergo open-closed transitions, and the simulation results (i.e., simulated transition pathways) are compared with those of another technique, to demonstrate that ICONGENI can explore highly reliable pathways in terms of thermal and chemical stability. Furthermore, we generate an ensemble of transition pathways through ICONGENI and investigate the possibility of using this method to reveal the transition mechanisms even when there are unknown metastable states on rough energy landscapes.

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Structural Insights into the Allosteric site of Arabidopsis NADP-Malic Enzyme 2: Role of the Second Sphere Residues in the Regulatory Signal Transmission

10.21203/rs.3.rs-256060/v1 ◽

2021 ◽

Author(s):

Mariel Claudia Gerrard Wheeler ◽

Cintia Lucía Arias ◽

Juliana Juliana da Fonseca Rezende e Mello ◽

Nuria Cirauqui Diaz ◽

Carlos Rangel Rodrigues ◽

...

Keyword(s):

Normal Mode ◽

Conformational Changes ◽

Active Site ◽

Normal Mode Analysis ◽

Signal Transmission ◽

Allosteric Regulation ◽

3D Structure ◽

Mode Analysis ◽

Allosteric Site ◽

Structural Determinants

Abstract Structure-function studies contribute to deciphering how small modifications in the primary structure could introduce desirable characteristics into enzymes without affecting its overall functioning. Malic enzymes (ME) are ubiquitous and responsible for a wide variety of functions. The availability of a high number of ME crystal structures from different species facilitates comparisons between sequence and structure. Specifically, the structural determinants necessary for fumarate allosteric regulation of ME has been of particular interest. NADP-ME2 from Arabidopsis thaliana exhibits a distinctive and complex regulation by fumarate, acting as an activator or an inhibitor according to substrate and effector concentrations. However, the 3D structure for this enzyme is not yet reported. In this work, we characterized the NADP-ME2 allosteric site by structural modeling, molecular docking, normal mode analysis and mutagenesis. The regulatory site model and its docking analysis suggested that other C4 acids including malate, NADP-ME2 substrate, could also fit into fumarate’s pocket. Besides, a non-conserved cluster of hydrophobic residues in the second sphere of the allosteric site was identified. The substitution of one of those residues, L62, by a less flexible residue as tryptophan, resulted in a complete loss of fumarate activation and a reduction of substrate affinities for the active site. In addition, normal mode analysis indicated that conformational changes leading to the activation could originate in the region surrounding L62, extending through the allosteric site till the active site. Finally, the results in this work contribute to the understanding of structural determinants necessary for allosteric regulation providing new insights for enzyme optimization.

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Unveiling functional motions based on point mutations in biased signaling systems: A normal mode study on Nerve Growth Factor bound to TrkA

10.1101/584300 ◽

2019 ◽

Author(s):

Pedro Túlio De Resende Lara ◽

David Perahia ◽

Ana Lígia Scott ◽

Antonio Sergio Kimus Braz

Keyword(s):

Normal Mode ◽

Conformational Changes ◽

Structural Changes ◽

Normal Mode Analysis ◽

Methodological Approach ◽

Point Mutations ◽

Interaction Network ◽

Mode Analysis ◽

Biased Signaling ◽

Trka Receptors

Many receptors elicit signal transduction by activating multiple intracellular pathways. This transduction may be triggered by a nonspecific ligand, which simultaneously activates all receptor’s signaling paths. In addition, the binding of a biased ligand preferentially elicits one path over another, in a process called biased signaling. Identifying the functional motions related to each one of these distinct pathways have direct impact in the development of new efficient and specific drugs. Here we show how to detect functional motions considering the case of the NGF/TrkA-Ig2 complex. TrkA receptors activation mediated by NGF depends on specific structural motions that trigger neuronal growth, development and survival in nervous system. R221W mutation in the ngf gene impairs the nociceptive signaling. Here we show the wide spread structural effects of this mutation in the NGF/TrkA-Ig2 complex, leading to the deletion of collective motions important to TrkA activation of nociceptive signaling. Our results suggest that subtle changes in the interaction network within neurotrophic factors due to the point mutation are sufficient to inhibit necessary conformational changes for TrkA receptors activation. The methodological approach presented in this article based conjunctively on normal mode analysis and the experimentally observed functional alterations due to point mutations provides an essential tool for unveiling the structural changes and motions related to the disease, that in turn could be important for a drug design study.

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Versatility of Approximating Single-Particle Electron Microscopy Density Maps Using Pseudoatoms and Approximation-Accuracy Control

BioMed Research International ◽

10.1155/2016/7060348 ◽

2016 ◽

Vol 2016 ◽

pp. 1-11 ◽

Cited By ~ 4

Author(s):

Slavica Jonić ◽

Carlos Oscar S. Sorzano

Keyword(s):

Electron Microscopy ◽

Normal Mode ◽

Conformational Changes ◽

Normal Mode Analysis ◽

Approximation Error ◽

Mode Analysis ◽

Accuracy Control ◽

Approximation Accuracy ◽

Gaussian Functions ◽

Density Maps

Three-dimensional Gaussian functions have been shown useful in representing electron microscopy (EM) density maps for studying macromolecular structure and dynamics. Methods that require setting a desired number of Gaussian functions or a maximum number of iterations may result in suboptimal representations of the structure. An alternative is to set a desired error of approximation of the given EM map and then optimize the number of Gaussian functions to achieve this approximation error. In this article, we review different applications of such an approach that uses spherical Gaussian functions of fixed standard deviation, referred to as pseudoatoms. Some of these applications use EM-map normal mode analysis (NMA) with elastic network model (ENM) (applications such as predicting conformational changes of macromolecular complexes or exploring actual conformational changes by normal-mode-based analysis of experimental data) while some other do not use NMA (denoising of EM density maps). In applications based on NMA and ENM, the advantage of using pseudoatoms in EM-map coarse-grain models is that the ENM springs are easily assigned among neighboring grains thanks to their spherical shape and uniformed size. EM-map denoising based on the map coarse-graining was so far only shown using pseudoatoms as grains.

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Allosteric Conformational Transition in Adenylate Kinase: Dynamic Correlations and Implication for Allostery

Australian Journal of Chemistry ◽

10.1071/ch09449 ◽

2010 ◽

Vol 63 (3) ◽

pp. 405 ◽

Cited By ~ 8

Author(s):

Ming S. Liu ◽

Billy D. Todd ◽

Richard J. Sadus

Keyword(s):

Normal Mode ◽

Conformational Changes ◽

Adenylate Kinase ◽

Conformational Transition ◽

Normal Mode Analysis ◽

Coarse Grained ◽

Mode Analysis ◽

Elastic Network Model ◽

Protein Functions ◽

Correlated Motion

An essential aspect of protein science is to determine the deductive relationship between structure, dynamics, and various sets of functions. The role of dynamics is currently challenging our understanding of protein functions, both experimentally and theoretically. To verify the internal fluctuations and dynamics correlations in an enzyme protein undergoing conformational transitions, we have applied a coarse-grained dynamics algorithm using the elastic network model for adenylate kinase. Normal mode analysis reveals possible dynamical and allosteric pathways for the transition between the open and the closed states of adenylate kinase. As the ligands binding induces significant flexibility changes of the nucleotides monophosphate (NMP) domain and adenosine triphosphate (ATP) domain, the diagonalized correlation between different structural transition states shows that most correlated motions occur between the NMP domain and the helices surrounding the ATP domain. The simultaneous existence of positive and negative correlations indicates that the conformational changes of adenylate kinase take place in an allosteric manner. Analyses of the cumulated normal mode overlap coefficients and long-range correlated motion provide new insights of operating mechanisms and dynamics of adenylate kinase. They also suggest a quantitative dynamics criterion for determining the allosteric cooperativity, which may be applicable to other proteins.

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How alginate lyase produces quasi-monodisperse oligosaccharides: a normal mode analysis-based docking and molecular dynamics simulation study

10.1101/2021.07.25.452152 ◽

2021 ◽

Author(s):

Hengyue Xu ◽

Qi Gao ◽

Dengming Ming

Keyword(s):

Normal Mode ◽

Conformational Changes ◽

Catalytic Domain ◽

Degradation Products ◽

Normal Mode Analysis ◽

Alginate Lyase ◽

Dynamics Simulation ◽

Mode Analysis ◽

Health Food ◽

Industrial Processing

Polysaccharide degradation products are widely used in medicine, health food, textile and other industries. The preparation of monosaccharides by enzymatic degradation is a key technology in bio industrial production. Unfortunately, most of the known digested products are complex oligosaccharide mixtures, which limit their industrial processing and application. In this study, we explored a docking technique based on normal mode analysis to examine the possible cleavage mechanism of an alginate lyase (AlyB) from Birio Splendidus, which contains the catalytic domain of polysaccharide lyase family 7 (PL7) and a CBM32 sugar binding module, and was observed to produce trisaccharide products with quasi-monosaccharide distribution. We compared the molecular interactions of the enzyme with the natural alginates, the polyMG whose products has the quasi-monodisperse distribution of tri-saccharide and two synthetic polysaccharides, the polyM and polyG whose products has a wider distribution of oligosaccharides. Our calculations quantitatively show that there are a series of deterministic conformational changes in the catalytic pocket, which control the specificity of the substrate; at the same time, it determines the uniformity of the final product together with the spatial position of the key catalytic sites. The dynamic simulations revealed that CBM domain plays a key role in assisting the release of tri-saccharides. Our data highlights the important role of enzyme flexibility in determining product uniformity, which may provide new insight into design of enzymes for the production of high-value mono-distributed oligosaccharides.

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HEMNMA-3D: Cryo Electron Tomography Method Based on Normal Mode Analysis to Study Continuous Conformational Variability of Macromolecular Complexes

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.663121 ◽

2021 ◽

Vol 8 ◽

Author(s):

Mohamad Harastani ◽

Mikhail Eltsov ◽

Amélie Leforestier ◽

Slavica Jonic

Keyword(s):

Data Analysis ◽

Rigid Body ◽

Normal Mode ◽

Conformational Changes ◽

Electron Tomography ◽

Normal Mode Analysis ◽

Mode Analysis ◽

Macromolecular Complexes ◽

Conformational Variability

Cryogenic electron tomography (cryo-ET) allows structural determination of biomolecules in their native environment (in situ). Its potential of providing information on the dynamics of macromolecular complexes in cells is still largely unexploited, due to the challenges of the data analysis. The crowded cell environment and continuous conformational changes of complexes make difficult disentangling the data heterogeneity. We present HEMNMA-3D, which is, to the best of our knowledge, the first method for analyzing cryo electron subtomograms in terms of continuous conformational changes of complexes. HEMNMA-3D uses a combination of elastic and rigid-body 3D-to-3D iterative alignments of a flexible 3D reference (atomic structure or electron microscopy density map) to match the conformation, orientation, and position of the complex in each subtomogram. The elastic matching combines molecular mechanics simulation (Normal Mode Analysis of the 3D reference) and experimental, subtomogram data analysis. The rigid-body alignment includes compensation for the missing wedge, due to the limited tilt angle of cryo-ET. The conformational parameters (amplitudes of normal modes) of the complexes in subtomograms obtained through the alignment are processed to visualize the distribution of conformations in a space of lower dimension (typically, 2D or 3D) referred to as space of conformations. This allows a visually interpretable insight into the dynamics of the complexes, by calculating 3D averages of subtomograms with similar conformations from selected (densest) regions and by recording movies of the 3D reference's displacement along selected trajectories through the densest regions. We describe HEMNMA-3D and show its validation using synthetic datasets. We apply HEMNMA-3D to an experimental dataset describing in situ nucleosome conformational variability. HEMNMA-3D software is available freely (open-source) as part of ContinuousFlex plugin of Scipion V3.0 (http://scipion.i2pc.es).

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Predicting protein functional motions: an old recipe with a new twist

10.1101/703652 ◽

2019 ◽

Cited By ~ 1

Author(s):

Sergei Grudinin ◽

Elodie Laine ◽

Alexandre Hoffmann

Keyword(s):

Normal Mode ◽

Conformational Changes ◽

Normal Mode Analysis ◽

Normal Modes ◽

Low Frequency ◽

Structural Heterogeneity ◽

Mode Analysis ◽

Protein Motions ◽

Wide Range ◽

Geometrical Constraints

Large macromolecules, including proteins and their complexes, very often adopt multiple conformations. Some of them can be seen experimentally, for example with X-ray crystallography or cryo-electron microscopy. This structural heterogeneity is not occasional and is frequently linked with specific biological function. Thus, the accurate description of macromolecular conformational transitions is crucial for understanding fundamental mechanisms of life’s machinery. We report on a real-time method to predict such transitions by extrapolating from instantaneous eigen-motions, computed using the normal mode analysis, to a series of twists. We demonstrate the applicability of our approach to the prediction of a wide range of motions, including large collective opening-closing transitions and conformational changes induced by partner binding. We also highlight particularly difficult cases of very small transitions between crystal and solution structures. Our method guaranties preservation of the protein structure during the transition and allows to access conformations that are unreachable with classical normal mode analysis. We provide practical solutions to describe localized motions with a few low-frequency modes and to relax some geometrical constraints along the predicted transitions. This work opens the way to the systematic description of protein motions, whatever their degree of collectivity. Our method is available as a part of the NOn-Linear rigid Block (NOLB) package at https://team.inria.fr/nano-d/software/nolb-normal-modes/.Significance StatementProteins perform their biological functions by changing their shapes and interacting with each other. Getting access to these motions is challenging. In this work, we present a method that generates plausible physics-based protein motions and conformations. We model a protein as a network of atoms connected by springs and deform it along the least-energy directions. Our main contribution is to perform the deformations in a nonlinear way, through a series of twists. This allows us to produce a wide range of motions, some of them previously inaccessible, and to preserve the structure of the protein during the motion. We are able to simulate the opening or closing of a protein and the changes it undergoes to adapt to a partner.

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STRUCTURAL AND FUNCTIONAL IMPACT OF G2032R MUTATION IN ROS1 – A THEORETICAL PERSPECTIVE

Asian Journal of Pharmaceutical and Clinical Research ◽

10.22159/ajpcr.2017.v10i5.17661 ◽

2017 ◽

Vol 10 (5) ◽

pp. 339

Author(s):

Anish Kumar

Keyword(s):

Drug Resistance ◽

Molecular Docking ◽

Normal Mode ◽

Conformational Changes ◽

Md Simulation ◽

Normal Mode Analysis ◽

Computational Simulation ◽

Theoretical Perspective ◽

Mode Analysis ◽

Protein Data Bank Code

Objective: Drug resistance is an imperative issue in the treatment of patients with lung cancer. In this work, investigation of the drug resistance mechanism of G2032R mutation in ROS1 is carried out using computational simulation techniques.Methods: Molecular docking and molecular dynamics (MD) simulation approach have been utilized to uncover the mechanism behind crizotinib resistance in ROS1 at a molecular level. Normal mode analysis was carried out using ElNemo server which examines the movements and conformational changes in the protein structure. ArgusLab, PEARLS, and Autodock were employed for the docking analysis, whereas GROMACS package 4.5.3 was used for MD simulation approach.Results: The results from our analysis indicates that wild-type ROS1 (Protein Data Bank Code 3ZBF) could be more crucial for the crizotinib binding as it indicates largest binding affinity, minimum number of H-bonds, and higher flexibility than mutant-type ROS1. Moreover, the theoretical basis for the cause of drug insensitivity is the differences in the electrostatic properties of binding site residues between the wild and mutant ROS1 structures. Our analysis theoretically suggests that E-2027 is a key residue responsible for the ROS1 drug selectivity.Conclusion: Molecular docking and MD simulation results provide an explanation of the resistance caused by G2032R and may give a key clue for the drug design to encounter drug resistance.Keywords: ROS1, Crizotinib resistance, Molecular docking, Normal mode analysis, Molecular dynamic simulation.

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